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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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DOE OSTI2020

Machine learning and ligand binding predictions: A review of data, methods, and obstacles

We report that computational predictions of ligand binding is a difficult problem, with more accurate methods being extremely computationally expensive. The use of machine learning for drug binding predictions could possibly leverage the use of biomedical big data in exchange for time-intensive simulations. This paper reviews current trends in the use of machine learning for drug binding predictions, data sources to develop machine learning algorithms, and potential problems that may lead to overfitting and ungeneralizable models. A few popular datasets that can be used to develop virtual high-throughput screening models are characterized using spatial statistics to quantify potential biases. We can see from evaluating some common benchmarks that good performance correlates with models with high-predicted bias scores and models with low bias scores do not have much predictive power. A better understanding of the limits of available data sources and how to fix them will lead to more generalizable models that will lead to novel drug discovery.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Decoding the protein–ligand interactions using parallel graph neural networks

Abstract Protein–ligand interactions (PLIs) are essential for biochemical functionality and their identification is crucial for estimating biophysical properties for rational therapeutic design. Currently, experimental characterization of these properties is the most accurate method, however, this is very time-consuming and labor-intensive. A number of computational methods have been developed in this context but most of the existing PLI prediction heavily depends on 2D protein sequence data. Here, we present a novel parallel graph neural network (GNN) to integrate knowledge representation and reasoning for PLI prediction to perform deep learning guided by expert knowledge and informed by 3D structural data. We develop two distinct GNN architectures: $$\hbox {GNN}_{\mathrm{F}}$$ GNN F is the base implementation that employs distinct featurization to enhance domain-awareness, while $$\hbox {GNN}_{\mathrm{P}}$$ GNN P is a novel implementation that can predict with no prior knowledge of the intermolecular interactions. The comprehensive evaluation demonstrated that GNN can successfully capture the binary interactions between ligand and protein’s 3D structure with 0.979 test accuracy for $$\hbox {GNN}_{\mathrm{F}}$$ GNN F and 0.958 for $$\hbox {GNN}_{\mathrm{P}}$$ GNN P for predicting activity of a protein–ligand complex. These models are further adapted for regression tasks to predict experimental binding affinities and $$\hbox {pIC}_{\mathrm{50}}$$ pIC 50 crucial for compound’s potency and efficacy. We achieve a Pearson correlation coefficient of 0.66 and 0.65 on experimental affinity and 0.50 and 0.51 on $$\hbox {pIC}_{\mathrm{50}}$$ pIC 50 with $$\hbox {GNN}_{\mathrm{F}}$$ GNN F and $$\hbox {GNN}_{\mathrm{P}}$$ GNN P , respectively, outperforming similar 2D sequence based models. Our method can serve as an interpretable and explainable artificial intelligence (AI) tool for predicted activity, potency, and biophysical properties of lead candidates. To this end, we show the utility of $$\hbox {GNN}_{\mathrm{P}}$$ GNN P on SARS-Cov-2 protein targets by screening a large compound library and comparing the prediction with the experimentally measured data.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Highly-scalable, physics-informed GANs for learning solutions of stochastic PDEs

Uncertainty quantification for forward and inverse problems is a central challenge across physical and biomedical disciplines. We address this challenge for the problem of modeling subsurface flow at the Hanford Site by combining stochastic computational models with observational data using physics-informed GAN models. The geographic extent, spatial heterogeneity, and multiple correlation length scales of the Hanford Site require training a computationally intensive GAN model to thousands of dimensions. We develop a highly optimized implementation that scales to {\herogpucount} NVIDIA Volta GPUs. We develop a hierarchical scheme based on a multi-player game-theoretic approach for exploiting domain parallelism, map discriminators and generators to multiple GPUs, and employ efficient communication schemes to ensure training stability and convergence. Our implementation scales to {\heronodecount} nodes on the Summit supercomputer with a \weakscalingeff\% scaling efficiency, achieving peak and sustained half-precision rates of {\heropeakperf} PF/s and {\herosustainedperf} PF/s.

physics informed ML, machine learning, generative ↗

DOE OSTI2018

Blazing Signature Filter: a library for fast pairwise similarity comparisons

Identifying similarities between datasets is a fundamental task in data mining and has become an integral part of modern scientific investigation. Whether the task is to identify co-expressed genes in large-scale expression surveys or to predict combinations of gene knockouts which would elicit a similar phenotype, the underlying computational task is often a multi-dimensional similarity test. As datasets continue to grow, improvements to the efficiency, sensitivity or specificity of such computation will have broad impacts as it allows scientists to more completely explore the wealth of scientific data. A significant practical drawback of large-scale data mining is the vast majority of pairwise comparisons are unlikely to be relevant, meaning that they do not share a signature of interest. It is therefore essential to efficiently identify these unproductive comparisons as rapidly as possible and exclude them from more time-intensive similarity calculations. The Blazing Signature Filter (BSF) is a highly efficient pairwise similarity algorithm which enables extensive data mining within a reasonable amount of time. The algorithm transforms datasets into binary metrics, allowing it to utilize the computationally efficient bit operators and provide a coarse measure of similarity. As a result, the BSF can scale to high dimensionality and rapidly filter unproductive pairwise comparison. Furthermore, two bioinformatics applications of the tool are presented to demonstrate the ability to scale to billions of pairwise comparisons and the usefulness of this approach.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Recommended Nuclear Structure and Decay Data for A=206 Isobars

Here, evaluated nuclear structure and decay data for all nuclei with mass number A=206 ( 206 Pt, 206 Au, 206 Hg, 206 Tl, 206 Pb, 206 Bi, 206 Po, 206 At, 206 Rn, 206 Fr, 206 Ra and 206 Ac), are presented. All available experimental data are compiled and evaluated, and best values for level and γ-ray energies, quantum numbers, lifetimes, γ-ray intensities and transition probabilities, as well as other nuclear properties, are recommended. Inconsistencies and discrepancies that exist in the literature are discussed. A number of computer codes (https://www-nds.iaea.org/public/ensdf_pgm/) developed by members of the NSDD network were used during the evaluation process. This work supersedes the earlier evaluation by F.G. Kondev (2008Ko21), published in Nuclear Data Sheets 109, 1527 (2008).

Kondev, F. G. [Argonne National Laboratory (ANL), ↗

DOE OSTI2016

HIGH-RESOLUTION ROTATIONAL SPECTRUM, DUNHAM COEFFICIENTS, AND POTENTIAL ENERGY FUNCTION OF NaCl

We report laboratory spectroscopy for the first time of the J = 1–0 and J = 2–1 lines of Na{sup 35}Cl and Na{sup 37}Cl in several vibrational states. The hyperfine structure has been resolved in both transitions for all vibrational levels, which permit us to predict with high accuracy the hyperfine splitting of the rotational transitions of the two isotopologues at higher frequencies. The new data have been merged with all previous works at microwave, millimeter, and infrared wavelengths and fitted to a series of mass-independent Dunham parameters and to a potential energy function. The obtained parameters have been used to compute a new dipole moment function, from which the dipole moment for infrared transitions up to Δ v = 8 has been derived. Frequency and intensity predictions are provided for all rovibrational transitions up to J = 150 and v = 8, from which the ALMA data of evolved stars can be modeled and interpreted.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2016

McStas Analysis of Monoenergetic Thermal Neutron Beam Generation for Total Cross Section Measurements

The thermal neutron scattering law (TSL) of a given material represents data that is essential for assessing the criticality safety of a neutronic system in which this material is utilized. Traditionally, the TSL is developed through elaborate calculations that combine input and models based on condensed matter physics and scattering theory. Nonetheless, measurements of key parameters (e.g., the total cross section at low energies) can help in benchmarking and validating TSL libraries such as those used in the ENDF/B database. In this work, the setup of experiments, at the PULSTAR reactor of North Carolina State University (NCSU), for creating monoenergetic thermal neutron beams in support of total scattering cross section measurements in the thermal energy range is explored using McStas simulations and experimental verification. A McStas model has been established of the NPD facility at the NCSU PULSTAR reactor to explore the production of monoenergetic thermal neutron beams in support of various applications including total cross section measurements. The McStas results clearly demonstrate the viability of six monochromatic thermal neutron beams with substantial intensities that allow future applications at the NPD facility. The experimental results reasonably support the computational model predictions. Based on these results, transmission thermal neutron experiments can be conducted for data validation studies. Furthermore, the model also allows the evaluation of design changes to expand the portfolio of available monoenergetic thermal neutron beams. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2016

ASA-FTL: An adaptive separation aware flash translation layer for solid state drives

Here, the flash-memory based Solid State Drive (SSD) presents a promising storage solution for increasingly critical data-intensive applications due to its low latency (high throughput), high bandwidth, and low power consumption. Within an SSD, its Flash Translation Layer (FTL) is responsible for exposing the SSD’s flash memory storage to the computer system as a simple block device. The FTL design is one of the dominant factors determining an SSD’s lifespan and performance. To reduce the garbage collection overhead and deliver better performance, we propose a new, low-cost, adaptive separation-aware flash translation layer (ASA-FTL) that combines sampling, data clustering and selective caching of recency information to accurately identify and separate hot/cold data while incurring minimal overhead. We use sampling for light-weight identification of separation criteria, and our dedicated selective caching mechanism is designed to save the limited RAM resource in contemporary SSDs. Using simulations of ASA-FTL with both real-world and synthetic workloads, we have shown that our proposed approach reduces the garbage collection overhead by up to 28% and the overall response time by 15% compared to one of the most advanced existing FTLs. We find that the data clustering using a small sample size provides significant performance benefit while only incurring a very small computation and memory cost. In addition, our evaluation shows that ASA-FTL is able to adapt to the changes in the access pattern of workloads, which is a major advantage comparing to existing fixed data separation methods.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

Study of titanate nanotubes by X-ray and electron diffraction and electron microscopy

The structure of titanate nanotubes (Ti-NTs) was studied by a combination of powder X-ray diffraction (PXRD), electron diffraction and high resolution transmission electron microscopy (HRTEM). Ti-NTs are prepared by hydrothermal treatment of TiO{sub 2} powder. The structure is identified by powder X-ray diffraction as the one based on the structure of H{sub 2}Ti{sub 2}O{sub 5}·H{sub 2}O phase. The same structure is obtained by projected potential from HRTEM through-focus image series. The structure is verified by simulated PXRD pattern with the aid of the Debye formula. The validity of the model is tested by computing Fourier transformation of a single nanotube which is proportional to measured electron diffraction intensities. A good agreement of this calculation with measured precession electron diffraction data is achieved. - Highlights: • Titanate nanotubes were prepared by hydrothermal method. • X-ray powder diffraction indicated their structure based on that of H{sub 2}Ti{sub 2}O{sub 5}·H{sub 2}O. • Structural model was created with the aid of high-resolution electron microscopy. • The model was verified with electron diffraction data. • X-ray powder diffraction pattern was calculated with the aid of the Debye formula.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Performance Analysis of Data Processing in Distributed File Systems with Near Data Processing

In the era of big data, the escalating volume and velocity of data generation pose significant challenges in data processing. Traditional systems like Spark and Hadoop manage the increasing amount and velocity of data by improving data placement and processing speeds. However, they face inherent limitations due to the essential data movement required for processing. In this paper, we explore the Skyhook framework, a novel extension of the Ceph distributed system, which significantly reduces the need for data movement. We present an extensive case study using the Skyhook framework, applying it with the TPC-H and K-means clustering algorithms. More specifically, we leverage the TPC-H benchmark to distinguish between CPU-intensive and I/O-intensive tasks. We explore the integration of K-means clustering into SQL, coupled with a near-data processing system to offload the computational burden of the K-means clustering algorithm to storage nodes. We conduct a comprehensive performance evaluation of distributed data processing applications across three processing approaches: traditional layout (baseline), optimized layout, and near-data processing. Additionally, we introduce the use of the FIO tool to simulate real-world system workloads, enabling the measurement of performance metrics such as average latency and CPU utilization. Our research is a significant advance in understanding how to optimize data processing systems to meet the demands of the modern data landscape.

Hou, Shiyue↗

DOE OSTI2021

Vibrational spectroscopy analysis of silica and silicate glass networks

Vibrational spectroscopy has been widely used to investigate various structural aspects of the glass network, and there are a plethora of papers reporting subtle but consistent changes in infrared and Raman spectral features of glass upon alterations of glass compositions, thermal histories, mechanical stresses, or surface treatments. However, interpretations of such spectral features are still obscured due to the lack of well-established physical principles accurately describing vibrational modes of the non-crystalline glass network. Due to the non-equilibrium nature of the glass network, three-dimensionally connected without any long-range orders, vibrational spectral features of glass cannot be interpreted using the analogy with those of isolated molecular moieties or crystalline counterparts. Here, this feature article explains why such comparisons are outdated and describes the recent advances made from theoretical calculations of vibrational spectral features of amorphous networks or comparisons of computational results with experimental data. For the interpretation of vibrational spectral features of silica and silicate glasses, the following empirical relationships are suggested: (i) the intensity-weighted peak position of the Si-O-Si stretch mode negatively correlates with the weighted average of the Si-O bond length distribution, and (ii) the broad band of the Si-O-Si bending mode negatively correlates with the Si-O-Si bond angle distribution. Selected examples of vibrational spectroscopic imaging of surface defects are discussed to deliberate the implication of these findings in the structure-property relationship of silica and silicate glass materials. Unanswered questions and continuing research challenges are identified.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2013

Is ExacTrac x-ray system an alternative to CBCT for positioning patients with head and neck cancers?

Purpose: To evaluate the usefulness of a six-degrees-of freedom (6D) correction using ExacTrac robotics system in patients with head-and-neck (HN) cancer receiving radiation therapy.Methods: Local setup accuracy was analyzed for 12 patients undergoing intensity-modulated radiation therapy (IMRT). Patient position was imaged daily upon two different protocols, cone-beam computed tomography (CBCT), and ExacTrac (ET) images correction. Setup data from either approach were compared in terms of both residual errors after correction and punctual displacement of selected regions of interest (Mandible, C2, and C6 vertebral bodies).Results: On average, both protocols achieved reasonably low residual errors after initial correction. The observed differences in shift vectors between the two protocols showed that CBCT tends to weight more C2 and C6 at the expense of the mandible, while ET tends to average more differences among the different ROIs.Conclusions: CBCT, even without 6D correction capabilities, seems preferable to ET for better consistent alignment and the capability to see soft tissues. Therefore, in our experience, CBCT represents a benchmark for positioning head and neck cancer patients.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2019

Potential Energy Implications of Connected and Automated Vehicles: Exploring Key Leverage Points through Scenario Screening and Analysis

Connected and automated vehicle (CAV) technologies could transform the transportation system over the coming decades, but face vehicle and systems engineering challenges, as well as technological, economic, demographic, and regulatory issues. The authors have developed a system dynamics model for generating, analyzing, and screening self-consistent CAV adoption scenarios. Results can support selection of scenarios for subsequent computationally intensive study using higher-resolution models. The potential for and barriers to large-scale adoption of CAVs have been analyzed using preliminary quantitative data and qualitative understandings of system relationships among stakeholders across the breadth of these issues. Although they are based on preliminary data, the results map possibilities for achieving different levels of CAV adoption and system-wide fuel use and demonstrate the interplay of behavioral parameters such as how consumers value their time versus financial parameters such as operating cost. By identifying the range of possibilities, estimating the associated energy and transportation service outcomes, and facilitating screening of scenarios for more detailed analysis, this work could inform transportation planners, researchers, and regulators.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2017

Large Eddy Simulation of turbulent flow in rod bundle with spacer grids

Pressurized water nuclear reactor fuel assemblies are made of fuel rods held by spacer grids, which are the core components of the nuclear power plants. Hot fuel rods are cooled by the coolant water flow, and the spacer grids with mixing vanes distort the mainstream, producing the swirling flow which can enhance the heat transfer to improve CHF (Critical Heat Flux). Heat transfer between fuel rods and coolant is a crucial part of thermal-hydraulic analysis. For the purpose to improve the thermal hydraulic performance of the fuel assemblies, many experiments have been conducted to understand the flow structures and three-dimensional behaviors of the turbulence in the rod bundle sub-channels and then to optimize the design of the spacer grid. In the experimental work, which requires lots of efforts to get reliable data, LDA (Laser Doppler Anemometry) and PIV (Particle Image Velocimetry) are generally used to measure the velocity profile and turbulent intensity in the sub-channels. Computational Fluid Dynamics (CFD) is another useful way to study the characteristics of the detailed flow condition and heat transfer phenomena in the subchannels. The main issue of the single-phase CFD is to accurately predict the flow and turbulence characteristics. RANS method is generally used to simulate the induced lateral velocity and the heat transfer process. With the development of computer technology, some more precise but previously time-consuming turbulent models, such as LES (Large Eddy Simulation), are gradually used for the simulation of rod bundle flow with current advanced CPU resources. Ikeno and Kajishima explained the decay of swirling turbulent flow in the rod bundle using LES method. Benhamadouche acquired the turbulence induced forces on the central rod of the rod bundle through performing the LES of the flow downstream the spacer grid. Chang and Tavoularis conducted hybrid simulations with SAS SST and LES of a 5 x 5 rod bundle, and several vortices were identified in the vicinity of the vanes and the generation mechanisms, evolution progress and influence on the velocities of these vortices were clarified. In the paper we present CFD simulations of turbulent flow in rod bundle sub-channels with spacer grids of two different experiments. One is MATiS-H benchmark experiment with scaled spacer grids, which is conducted by KAERI, and is used as a CFD benchmark test, and the other is a 5 x 5 rod bundle with typical spacer grids using PIV technology, with the cooperation of Harbin Engineering University. The main objectives of the calculations are to validate LES methodology by the benchmark experiments.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2019

PREDICTION OF CYCLIC VARIABILITY AND KNOCK-LIMITED SPARK ADVANCE (KLSA) IN SPARK-IGNITION (SI) ENGINE

Engine knock remains one of the major barriers to further improve the thermal efficiency of spark-ignition (SI) engines. SI engine is usually operated at knock-limited spark advance (KLSA) to achieve possibly maximum efficiency with given engine hardware and fuel properties. Co-optimization of fuels and engines is promising to improve engine efficiency, and predictive computational fluid dynamics (CFD) models can be used to facilitate this process. However, cyclic variability of SI engine demands that multi cycle results are required to capture the extreme conditions. In addition, Mach Courant Friedrichs-Lewy (CFL) number of 1 is desired to accurately predict the knock intensity (KI), resulting in unaffordable computational cost. In this study, a new approach to numerically predict KLSA using large Mach CFL of 50 with ten consecutive cycle simulation is proposed. This approach is validated against the experimental data for a boosted SI engine at multiple loads and spark timings with good agreements in terms of cylinder pressure, combustion phasing, and cyclic variation. Engine knock is predicted with early spark timing, indicated by significant pressure oscillation and end-gas heat release. Maximum amplitude of pressure oscillation analysis is performed to quantify the KI, and the slope change point in KI extrema is used to indicate the KLSA accurately. Using a smaller Mach CFL number of 5 also results in the same conclusions, thus demonstrating that this approach is insensitive to the Mach CFL number. The use of large Mach CFL number allows us to achieve fast turn-around time for multicycle engine CFD simulations.

CCV↗

DOE OSTI2023

Nuclear Data Sheets for A=201

Evaluated nuclear structure and decay data for all nuclei with mass number A=201 ( 201 Os, 201 Ir, 201 Pt, 201 Au, 201 Hg, 201 Tl, 201 Pb, 201 Bi, 201 Po, 201 At, 201 Rn, 201 Fr, 201 Ra) are presented. All available experimental data are compiled and evaluated, and best values for level and γ-ray energies, quantum numbers, lifetimes, γ-ray intensities and transition probabilities, as well as other nuclear properties, are recommended. Inconsistencies and discrepancies that exist in the literature are discussed. A number of computer codes (https://wwwnds.iaea.org/public/ensdf pgm/index.htm) developed by members of the NSDD network were used during the evaluation process. For example, the reported absolute γ-ray emission probabilities and their uncertainties in various decay data sets were determined using the GABS code. The γ-ray transition probabilities were determined using the RULER code and the corresponding uncertainties were determined using a Monte-Carlo approach. In conclusion, this work supersedes the earlier evaluation by F.G. Kondev (2007Ko06), published in Nuclear Data Sheets 108, 365 (2007).

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

Gaussian process analysis of electron energy loss spectroscopy data: multivariate reconstruction and kernel control

Abstract Advances in hyperspectral imaging including electron energy loss spectroscopy bring forth the challenges of exploratory and physics-based analysis of multidimensional data sets. The multivariate linear unmixing methods generally explore similarities in the energy dimension, but ignore correlations in the spatial domain. At the same time, Gaussian process (GP) explicitly incorporate spatial correlations in the form of kernel functions but is computationally intensive. Here, we implement a GP method operating on the full spatial domain and reduced representations in the energy domain. In this multivariate GP, the information between the components is shared via a common spatial kernel structure, while allowing for variability in the relative noise magnitude or image morphology. We explore the role of kernel constraints on the quality of the reconstruction, and suggest an approach for estimating them from the experimental data. We further show that spatial information contained in higher-order components can be reconstructed and spatially localized.

36 MATERIALS SCIENCE↗

DOE OSTI2018

High-Performance Multi-Mode Ptychography Reconstruction on Distributed GPUs

Abstract—Ptychography is an emerging imaging technique that is able to provide wavelength-limited spatial resolution from spec-imen with extended lateral dimensions. As a scanning microscopy method, a typical two-dimensional image requires a number of data frames. As a diffraction-based imaging technique, the real-space image has to be recovered through iterative reconstruction algorithms. Due to these two inherent aspects, a ptychographic reconstruction is generally a computation-intensive and time-consuming process, which limits the throughput of this method. We report an accelerated version of the multi-mode difference map algorithm for ptychography reconstruction using multiple distributed GPUs. This approach leverages available scientific computing packages in Python, including mpi4py and PyCUDA, with the core computation functions implemented in CUDA C. We find that interestingly even with MPI collective communications, the weak scaling in the number of GPU nodes can still remain nearly constant. Most importantly, for realistic diffraction measurements, we observe a speedup ranging from a factor of 10 to 103 depending on the data size, which reduces the reconstruction time remarkably from hours to typically about 1 minute and is thus critical for real-time data processing and visualization.

97 MATHEMATICS AND COMPUTING↗